Created
September 25, 2019 10:00
-
-
Save bsipos/1359a6b55b8b3903f19bef19d451fb18 to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/bin/bash | |
INPUT_FQ=demo_reads.fq | |
TRANSCRIPTOME="transcriptome.fas" | |
COUNT_TSV="online_counts.tsv" | |
COUNT_MONITOR="[ -f $COUNT_TSV ] && ( csvtk -t watch -O sec_dist.pdf -B 100 -f SecCount $COUNT_TSV ; sleep 2)" # script to monitor secondary read count distribution | |
csvtk cat $INPUT_FQ \ | |
| seqkit seq -Q 3 \ | |
| seqkit watch -x -f MeanQual -p 20000 \ | |
| minimap2 -t 20 -K 100k -ax map-ont $TRANSCRIPTOME - 2>/dev/null| samtools view -b \ | |
| seqkit bam -B 3 -f IsSec -W 4 -x -p 4000 \ | |
| seqkit bam -Q -m 1 -x -p 600000 -c $COUNT_TSV -e "$COUNT_MONITOR" \ | |
| samtools sort -o sorted_aln.bam - | |
samtools index sorted_aln.bam; |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment